理学最新文献

{"title":"Effects of dietary Lactobacillus postbiotics and bacitracin on the modulation of mucosa-associated microbiota and pattern recognition receptors affecting immunocompetence of jejunal mucosa in pigs challenged with enterotoxigenic F18⁺ Escherichia coli.","authors":"Marcos Elias Duarte, Zixiao Deng, Sung Woo Kim","doi":"10.1186/s40104-024-01098-1","DOIUrl":"10.1186/s40104-024-01098-1","url":null,"abstract":"<p><strong>Background: </strong>Enterotoxigenic Escherichia coli (E. coli) is a threat to humans and animals that causes intestinal disorders. Antimicrobial resistance has urged alternatives, including Lactobacillus postbiotics, to mitigate the effects of enterotoxigenic E. coli.</p><p><strong>Methods: </strong>Forty-eight newly weaned pigs were allotted to NC: no challenge/no supplement; PC: F18⁺ E. coli challenge/no supplement; ATB: F18⁺ E. coli challenge/bacitracin; and LPB: F18⁺ E. coli challenge/postbiotics and fed diets for 28 d. On d 7, pigs were orally inoculated with F18⁺ E. coli. At d 28, the mucosa-associated microbiota, immune and oxidative stress status, intestinal morphology, the gene expression of pattern recognition receptors (PRR), and intestinal barrier function were measured. Data were analyzed using the MIXED procedure in SAS 9.4.</p><p><strong>Results: </strong>PC increased (P < 0.05) Helicobacter mastomyrinus whereas reduced (P < 0.05) Prevotella copri and P. stercorea compared to NC. The LPB increased (P < 0.05) P. stercorea and Dialister succinatiphilus compared with PC. The ATB increased (P < 0.05) Propionibacterium acnes, Corynebacterium glutamicum, and Sphingomonas pseudosanguinis compared to PC. The PC tended to reduce (P = 0.054) PGLYRP4 and increased (P < 0.05) TLR4, CD14, MDA, and crypt cell proliferation compared with NC. The ATB reduced (P < 0.05) NOD1 compared with PC. The LPB increased (P < 0.05) PGLYRP4, and interferon-γ and reduced (P < 0.05) NOD1 compared with PC. The ATB and LPB reduced (P < 0.05) TNF-α and MDA compared with PC.</p><p><strong>Conclusions: </strong>The F18⁺ E. coli challenge compromised intestinal health. Bacitracin increased beneficial bacteria showing a trend towards increasing the intestinal barrier function, possibly by reducing the expression of PRR genes. Lactobacillus postbiotics enhanced the immunocompetence of nursery pigs by increasing the expression of interferon-γ and PGLYRP4, and by reducing TLR4, NOD1, and CD14.</p>","PeriodicalId":64067,"journal":{"name":"Journal of Animal Science and Biotechnology","volume":"15 1","pages":"139"},"PeriodicalIF":6.3,"publicationDate":"2024-10-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11468193/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142402153","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Quantitative phase microscopies: accuracy comparison","authors":"Patrick C. Chaumet, Pierre Bon, Guillaume Maire, Anne Sentenac, Guillaume Baffou","doi":"10.1038/s41377-024-01619-7","DOIUrl":"https://doi.org/10.1038/s41377-024-01619-7","url":null,"abstract":"<p>Quantitative phase microscopies (QPMs) play a pivotal role in bio-imaging, offering unique insights that complement fluorescence imaging. They provide essential data on mass distribution and transport, inaccessible to fluorescence techniques. Additionally, QPMs are label-free, eliminating concerns of photobleaching and phototoxicity. However, navigating through the array of available QPM techniques can be complex, making it challenging to select the most suitable one for a particular application. This tutorial review presents a thorough comparison of the main QPM techniques, focusing on their accuracy in terms of measurement precision and trueness. We focus on 8 techniques, namely digital holographic microscopy (DHM), cross-grating wavefront microscopy (CGM), which is based on QLSI (quadriwave lateral shearing interferometry), diffraction phase microscopy (DPM), differential phase-contrast (DPC) microscopy, phase-shifting interferometry (PSI) imaging, Fourier phase microscopy (FPM), spatial light interference microscopy (SLIM), and transport-of-intensity equation (TIE) imaging. For this purpose, we used a home-made numerical toolbox based on discrete dipole approximation (IF-DDA). This toolbox is designed to compute the electromagnetic field at the sample plane of a microscope, irrespective of the object’s complexity or the illumination conditions. We upgraded this toolbox to enable it to model any type of QPM, and to take into account shot noise. In a nutshell, the results show that DHM and PSI are inherently free from artefacts and rather suffer from coherent noise; In CGM, DPC, DPM and TIE, there is a trade-off between precision and trueness, which can be balanced by varying one experimental parameter; FPM and SLIM suffer from inherent artefacts that cannot be discarded experimentally in most cases, making the techniques not quantitative especially for large objects covering a large part of the field of view, such as eukaryotic cells.</p>","PeriodicalId":18069,"journal":{"name":"Light-Science & Applications","volume":"59 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-10-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142404911","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Light People: Prof. Daoxin Dai, Dr. Patrick Lo, and Prof. Yikai Su—innovators in silicon photonics","authors":"Yating Wan, Chenzi Guo","doi":"10.1038/s41377-024-01650-8","DOIUrl":"https://doi.org/10.1038/s41377-024-01650-8","url":null,"abstract":"<p>In this edition of <i>Light People</i>, we are excited to feature Prof. Daoxin Dai (Zhejiang University), Prof. Yikai Su (Shanghai Jiao Tong University), and Dr. Patrick Lo (Advanced Micro Foundry Pte Ltd, Singapore), three prominent researchers shaping the future of silicon photonics. Their collaborative work addresses critical issues in silicon photonics, including reducing propagation losses, enlarging the functionalities and enhancing building blocks, integrating efficient laser sources, expanding applications, and pushing the boundaries of optical and electronic integration. Through this interview, we delve into their academic journeys, challenges, and future visions, offering insights into the ongoing evolution of silicon photonics and its potential to transform industries. For a deeper exploration of their experiences and advice, the full interview is available in the Supplementary material.</p>","PeriodicalId":18069,"journal":{"name":"Light-Science & Applications","volume":"64 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-10-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142404910","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Bacillus CotA laccase improved the intestinal health, amino acid metabolism and hepatic metabolic capacity of Pekin ducks fed naturally contaminated AFB₁ diet.","authors":"Mingxin Ma, Qianqian Wang, Yanrong Liu, Guiming Li, Limeng Liu, Gaigai Wang, Yongpeng Guo, Shimeng Huang, Qiugang Ma, Cheng Ji, Lihong Zhao","doi":"10.1186/s40104-024-01091-8","DOIUrl":"10.1186/s40104-024-01091-8","url":null,"abstract":"<p><strong>Background: </strong>Aflatoxin B₁ (AFB₁) is a prevalent contaminant in agricultural products, presenting significant risks to animal health. CotA laccase from Bacillus licheniformis has shown significant efficacy in degrading mycotoxins in vitro test. The efficacy of Bacillus CotA laccase in animals, however, remains to be confirmed. A 2 × 2 factorial design was used to investigate the effects of Bacillus CotA laccase level (0 or 1 U/kg), AFB₁ challenge (challenged or unchallenged) and their interactions on ducks. The purpose of this study was to evaluate the efficacy of Bacillus CotA laccase in alleviating AFB₁ toxicosis of ducks.</p><p><strong>Results: </strong>Bacillus CotA laccase alleviated AFB₁-induced declines in growth performance of ducks accompanied by improved average daily gain (ADG) and lower feed/gain ratio (F/G). Bacillus CotA laccase ameliorated AFB₁-induced gut barrier dysfunctions and inflammation testified by increasing the jejunal villi height/crypt depth ratio (VH/CD) and the mRNA expression of tight junction protein 1 (TJP1) and zonula occluden-1 (ZO-1) as well as decreasing the expression of inflammation-related genes in the jejunum of ducks. Amino acid metabolome showed that Bacillus CotA laccase ameliorated AFB₁-induced amino acid metabolism disorders evidenced by increasing the level of glutamic acid in serum and upregulating the expression of amino acid transport related genes in jejunum of ducks. Bacillus CotA laccase ameliorated AFB₁-induced liver injury testified by suppressing oxidative stress, inhibiting apoptosis, and downregulating the expression of hepatic metabolic enzyme related genes of ducks. Moreover, Bacillus CotA laccase degraded AFB₁ in digestive tract of ducks, resulting in the reduced absorption level of AFB₁ across intestinal epithelium testified by the decreased level of AFB₁-DNA adduct in the liver, and the reduced content of AFB₁ residues in liver and feces of ducks.</p><p><strong>Conclusions: </strong>Bacillus CotA laccase effectively improved the growth performance, intestinal health, amino acid metabolism and hepatic aflatoxin metabolism of ducks fed AFB₁ diets, highlighting its potential as an efficient and safe feed enzyme for AFB₁ degradation in animal production.</p>","PeriodicalId":64067,"journal":{"name":"Journal of Animal Science and Biotechnology","volume":"15 1","pages":"138"},"PeriodicalIF":6.3,"publicationDate":"2024-10-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11465776/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142395628","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Excitation-wavelength-dependent persistent luminescence from single-component nonstoichiometric CaGaxO4:Bi for dynamic anti-counterfeiting","authors":"Bo-Mei Liu, Yue Lin, Yingchun Liu, Bibo Lou, Chong-Geng Ma, Hui Zhang, Jing Wang","doi":"10.1038/s41377-024-01635-7","DOIUrl":"https://doi.org/10.1038/s41377-024-01635-7","url":null,"abstract":"<p>Materials capable of dynamic persistent luminescence (PersL) within the visible spectrum are highly sought after for applications in display, biosensing, and information security. However, PersL materials with eye-detectable and excitation-wavelength-dependent characteristics are rarely achieved. Herein, a nonstoichiometric compound CaGa_xO₄:Bi (<i>x</i> &lt; 2) is present, which demonstrates ultra-long, color-tunable PersL. The persistent emission wavelength can be tuned by varying the excitation wavelength, enabling dynamic color modulation from the green to the orange region within the visible spectrum. Theoretical calculations, in conjunction with experimental observations, are utilized to elucidate the thermodynamic charge transitions of various defect states, thereby providing insights into the relationship between Bi³⁺ emitters, traps, and multicolored PersL. Furthermore, the utility of color-tunable PersL materials and flexible devices is showcased for use in visual sensing of invisible ultraviolet light, multicolor display, information encryption, and anti-counterfeiting. These discoveries create new opportunities to develop smart photoelectric materials with dynamically controlled PersL for various applications.</p>","PeriodicalId":18069,"journal":{"name":"Light-Science & Applications","volume":"24 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-10-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142397669","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Ultra-high brightness Micro-LEDs with wafer-scale uniform GaN-on-silicon epilayers","authors":"Haifeng Wu, Xiao Lin, Qin Shuai, Youliang Zhu, Yi Fu, Xiaoqin Liao, Yazhou Wang, Yizhe Wang, Chaowei Cheng, Yong Liu, Lei Sun, Xinyi Luo, Xiaoli Zhu, Liancheng Wang, Ziwei Li, Xiao Wang, Dong Li, Anlian Pan","doi":"10.1038/s41377-024-01639-3","DOIUrl":"https://doi.org/10.1038/s41377-024-01639-3","url":null,"abstract":"<p>Owing to high pixel density and brightness, gallium nitride (GaN) based micro-light-emitting diodes (Micro-LEDs) are considered revolutionary display technology and have important application prospects in the fields of micro-display and virtual display. However, Micro-LEDs with pixel sizes smaller than 10 μm still encounter technical challenges such as sidewall damage and limited light extraction efficiency, resulting in reduced luminous efficiency and severe brightness non-uniformity. Here, we reported high-brightness green Micro-displays with a 5 μm pixel utilizing high-quality GaN-on-Si epilayers. Four-inch wafer-scale uniform green GaN epilayer is first grown on silicon substrate, which possesses a low dislocation density of 5.25 × 10⁸ cm⁻², small wafer bowing of 16.7 μm, and high wavelength uniformity (standard deviation STDEV &lt; 1 nm), scalable to 6-inch sizes. Based on the high-quality GaN epilayers, green Micro-LEDs with 5 μm pixel sizes are designed with vertical non-alignment bonding technology. An atomic sidewall passivation method combined with wet treatment successfully addressed the Micro-LED sidewall damages and steadily produced nano-scale surface textures on the pixel top, which unlocked the internal quantum efficiency of the high-quality green GaN-on-Si epi-wafer. Ultra-high brightness exceeding 10⁷ cd/m² (nits) is thus achieved in the green Micro-LEDs, marking the highest reported results. Furthermore, integration of Micro-LEDs with Si-based CMOS circuits enables the realization of green Micro-LED displays with resolution up to 1080 × 780, realizing high-definition playback of movies and images. This work lays the foundation for the mass production of high-brightness Micro-LED displays on large-size GaN-on-Si epi-wafers.</p>","PeriodicalId":18069,"journal":{"name":"Light-Science & Applications","volume":"7 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142385081","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Deep learning with photonic neural cellular automata","authors":"Gordon H. Y. Li, Christian R. Leefmans, James Williams, Robert M. Gray, Midya Parto, Alireza Marandi","doi":"10.1038/s41377-024-01651-7","DOIUrl":"https://doi.org/10.1038/s41377-024-01651-7","url":null,"abstract":"<p>Rapid advancements in deep learning over the past decade have fueled an insatiable demand for efficient and scalable hardware. Photonics offers a promising solution by leveraging the unique properties of light. However, conventional neural network architectures, which typically require dense programmable connections, pose several practical challenges for photonic realizations. To overcome these limitations, we propose and experimentally demonstrate Photonic Neural Cellular Automata (PNCA) for photonic deep learning with sparse connectivity. PNCA harnesses the speed and interconnectivity of photonics, as well as the self-organizing nature of cellular automata through local interactions to achieve robust, reliable, and efficient processing. We utilize linear light interference and parametric nonlinear optics for all-optical computations in a time-multiplexed photonic network to experimentally perform self-organized image classification. We demonstrate binary (two-class) classification of images using as few as 3 programmable photonic parameters, achieving high experimental accuracy with the ability to also recognize out-of-distribution data. The proposed PNCA approach can be adapted to a wide range of existing photonic hardware and provides a compelling alternative to conventional photonic neural networks by maximizing the advantages of light-based computing whilst mitigating their practical challenges. Our results showcase the potential of PNCA in advancing photonic deep learning and highlights a path for next-generation photonic computers.</p>","PeriodicalId":18069,"journal":{"name":"Light-Science & Applications","volume":"2 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-10-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142384358","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Dietary ferulic acid supplementation enhances antioxidant capacity and alleviates hepatocyte pyroptosis in diquat challenged piglets.","authors":"Junqiu Luo, Xiu Wu, Daiwen Chen, Bing Yu, Jun He","doi":"10.1186/s40104-024-01086-5","DOIUrl":"10.1186/s40104-024-01086-5","url":null,"abstract":"<p><strong>Background: </strong>Oxidative stress significantly impacts growth performance and liver function in piglets. Ferulic acid (FA) works as an antioxidant, however, the role and mechanism of FA in the regulation of diquat-induced oxidative stress in piglets are less known. This study was designed to investigate the effects of FA on growth performance and antioxidant capacity in piglets with diquat challenge.</p><p><strong>Methods: </strong>Thirty-two healthy DLY (Duroc × Landrace × Yorkshire) piglets (13.24 ± 0.19 kg) were randomly divided into one of two diets including 0 or 4 g/kg FA for 14 d. On d 15, all pigs were intraperitoneally injected diquat or sterile saline.</p><p><strong>Results: </strong>Dietary supplementation with ferulic acid (FA) significantly improved the average daily gain (ADG) and decreased feed-gain ratio (F/G) of piglets. Here, dietary FA supplementation reduced serum aspartate aminotransferase (AST), alanine aminotransferase (ALT) activities in diquat challenged piglets. Furthermore, diquat infusion increased reactive oxygen radicals (ROS) level in liver, decreased the activities of total superoxide dismutase (T-SOD) and glutathione peroxidase (GSH-Px), total antioxidant capacity (T-AOC) and increased malondialdehyde (MDA) content in the liver and serum. Supplementation with FA significantly increased T-AOC and T-SOD activities and decreased MDA and ROS levels. FA down-regulated gene and protein expression of Keap1, and up-regulated protein expression of Nrf2 and HO-1 in the liver of piglets with diquat challenge. Importantly, diquat challenge increased the ratio of late apoptosis, increased serum levels of IL-1β, IL-18 and lactate dehydrogenase (LDH), and up-regulated pyroptosis-related genes in the liver. FA supplementation reduced the ratio of late apoptosis and down-regulated mRNA expression of Caspase-1. Accordingly, FA addition reduced concentration of IL-1β, IL-18, and LDH under diquat challenge.</p><p><strong>Conclusions: </strong>Diquat-induced oxidative stress reduced growth performance and impaired liver function in piglets. Dietary FA supplementation enhanced the antioxidant capacity and reduced the degree of hepatocyte pyroptosis, thereby alleviating the oxidative damage in the liver and mitigating the impact of diquat on growth performance of piglets.</p>","PeriodicalId":64067,"journal":{"name":"Journal of Animal Science and Biotechnology","volume":"15 1","pages":"134"},"PeriodicalIF":6.3,"publicationDate":"2024-10-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11457559/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142382584","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Dietary supplementation with pterostilbene activates the PI3K-AKT-mTOR signalling pathway to alleviate progressive oxidative stress and promote placental nutrient transport.","authors":"Mingming Cao, Liyun Bai, Haoyun Wei, Yantong Guo, Guodong Sun, Haoyang Sun, Baoming Shi","doi":"10.1186/s40104-024-01090-9","DOIUrl":"10.1186/s40104-024-01090-9","url":null,"abstract":"<p><strong>Background: </strong>Progressive oxidative stress easily occurs as a result of a gradual increase in the intensity of maternal metabolism due to rapid foetal development and increased intensity of lactation. However, studies on the effects of processive oxidative stress on nutrient transport in the placenta have received little attention. The present study was conducted on sows at 85 days of gestation to study the effects of pterostilbene (PTE) on maternal oxidative stress status and placental nutrient transport.</p><p><strong>Results: </strong>PTE increased the antioxidant capacity and immunoglobulin content in mothers' blood and milk, reduced the level of inflammatory factors, and improved the nutrient content of milk. PTE also reduced sow backfat loss and the number of weak sons, and increased piglet weaning weight and total weaning litter weight. We subsequently found that PTE enhanced placental glucose and fatty acid transport and further affected glycolipid metabolism by increasing the expression of LAL, PYGM, and Gbe-1, which activated the PI3K phosphorylation pathway. Moreover, PTE addition altered the relative abundance of the Firmicutes, Proteobacteria, Parabacillus, and Bacteroidetes-like RF16 groups in sow faeces. PTE increased the levels of acetate, propionate, butyrate and isovalerate in the faeces.</p><p><strong>Conclusions: </strong>These findings reveal that the addition of PTE during pregnancy and lactation mitigates the effects of processive oxidative stress on offspring development by altering maternal microbial and placental nutrient transport capacity.</p>","PeriodicalId":64067,"journal":{"name":"Journal of Animal Science and Biotechnology","volume":"15 1","pages":"133"},"PeriodicalIF":6.3,"publicationDate":"2024-10-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11456245/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142378657","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The goat pan-genome reveals patterns of gene loss during domestication.","authors":"Jiaxin Liu, Yilong Shi, Dongxin Mo, Lingyun Luo, Songsong Xu, Fenghua Lv","doi":"10.1186/s40104-024-01092-7","DOIUrl":"10.1186/s40104-024-01092-7","url":null,"abstract":"<p><strong>Background: </strong>Unveiling genetic diversity features and understanding the genetic mechanisms of diverse goat phenotypes are pivotal in facilitating the preservation and utilization of these genetic resources. However, the total genetic diversity within a species can't be captured by the reference genome of a single individual. The pan-genome is a collection of all the DNA sequences that occur in a species, and it is expected to capture the total genomic diversity of the specific species.</p><p><strong>Results: </strong>We constructed a goat pan-genome using map-to-pan assemble based on 813 individuals, including 723 domestic goats and 90 samples from their wild relatives, which presented a broad regional and global representation. In total, 146 Mb sequences and 974 genes were identified as absent from the reference genome (ARS1.2; GCF_001704415.2). We identified 3,190 novel single nucleotide polymorphisms (SNPs) using the pan-genome analysis. These novel SNPs could properly reveal the population structure of domestic goats and their wild relatives. Presence/absence variation (PAV) analysis revealed gene loss and intense negative selection during domestication and improvement.</p><p><strong>Conclusions: </strong>Our research highlights the importance of the goat pan-genome in capturing the missing genetic variations. It reveals the changes in genomic architecture during goat domestication and improvement, such as gene loss. This improves our understanding of the evolutionary and breeding history of goats.</p>","PeriodicalId":64067,"journal":{"name":"Journal of Animal Science and Biotechnology","volume":"15 1","pages":"132"},"PeriodicalIF":6.3,"publicationDate":"2024-10-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11453020/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142376313","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}